Research workbench
Interaction between vitamin D receptor and coactivator peptide SRC2-3
Analyse Interaction between vitamin D receptor and coactivator peptide SRC2-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H1E
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D3 receptor; Nuclear receptor coactivator 2 peptide
- UniProt
- P13053, Q15596
- Ligands
- VDX
- Pockets
- 3 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D3 receptor | protein | 239 | 67% helix, 2% strand | P13053 |
| C | Nuclear receptor coactivator 2 peptide | protein | 10 | 60% helix, 0% strand | Q15596 |
Ligands and binding sites
- VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-1,3-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.87 | 0.95 | 38 | VDX |
| 2 | 64 | 0.33 | 0.76 | 10 | empty |
| 3 | 61 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 566 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5H1E · Interaction between vitamin D receptor and coactivator peptide SRC2-3 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P13053
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 5H1E · PDBe 5H1E · UniProt P13053 · UniProt Q15596
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